[gmx-users] Reflecting Boundary Condition

atanu das samrucu at yahoo.co.in
Fri Feb 3 01:07:28 CET 2017

Dear Prof. van der Spoel,
Thanks a lot for your reply. As far as I understand, the wall potential implemented in gromacs, can only handle reflective boundary condition along one of the three dimensions. What I exactly want is to put reflecting boundary conditions on all the 3 directions. Let's assume a protein-in-water system, a cubic box with dimension of 5×5×5 nm3. Now, I want to restrict only the protein within a box of 3×3×3 nm3 (as if the protein is in a smaller virtual box within a larger real box). Is it possible to do that in gromacs?

    On Wednesday, 1 February 2017 11:42 PM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

 On 01/02/17 22:35, atanu das wrote:
> Hi All,
> Is there any way to implement reflecting boundary conditions in gromacs?
> ThanksAtanu
Check the manual for wall potential.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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